added appnote example

git-svn-id: https://dng.biozentrum.unibas.ch/svn/openstructure/trunk@2396 5a81b35b-ba03-0410-adc8-b2c5c5119f08

examples/seq/conservation.py

+from ost.seq import alg
+#-------------------------------------------------------------------------------
+# Loading structure and alignment
+#-------------------------------------------------------------------------------
+m=io.LoadPDB('sh2.pdb')
+mp=m.Select('ishetatm=false')
+aln=io.LoadAlignment('sh2.aln')
+aln.AttachView(0, mp)
+#-------------------------------------------------------------------------------
+# Calculate conservation of alignment
+#-------------------------------------------------------------------------------
+for r in m.residues:
+  r.SetFloatProp('cons', 0)
+alg.Conservation(aln)
+#-------------------------------------------------------------------------------
+# Setup Graphical Objects for Rendering
+#-------------------------------------------------------------------------------
+g=gfx.Entity('SH2', m)
+s=io.LoadSurface('sh2.vert')
+gs=gfx.Surface('SH2-surf', s)
+scene.Add(gs)
+scene.Add(g)
+scene.CenterOn(g)
+
+s.Attach(mp.Select('ishetatm=false'), 5.0)
+
+gr=gfx.Gradient()
+gr.SetColorAt(0.0, gfx.BLUE)
+gr.SetColorAt(0.5, gfx.WHITE)
+gr.SetColorAt(1.0, gfx.RED)
+gs.ColorBy('cons', gr, 0.8, 1.0, 
+           mol.Prop.Level.RESIDUE)
+g.SetRenderMode(gfx.HSC, 
+                m.Select('ishetatm=false'))
+g.SetRenderMode(gfx.CUSTOM, 
+                m.Select('ishetatm=true'))
+g.SetColor(gfx.YELLOW, 'ishetatm=true')
+
+
+seq_viewer=gui.SequenceViewer()
+seq_viewer.AddAlignment(aln)
+seq_viewer.Show()